Hello! I would guess that this is occurring for one of two reasons:
(1) There could be a shrink differential between the two materials, since there is such a greater volume of silicone than thermoplastic, the silicone could be warping the plastic as it shrinks.
(2) Depending on the temperature at which the silicone overmolding is taking place (if it is higher than the glass transition temperature of the thermoplastic) it could be releasing any stresses that were molded into plastic components when they were molded/extruded.
I would try overmolding the silicone at a lower temperature, and if there is any postbaking or postcuring process being performed try doing so with the parts under compression.
Thanks for your question, let me know if we can help you further!